## PC_ 1
## Positive: Hmgb2, Lgals1, S100a6, S100a4, Stmn1, Pclaf, Hist1h2ap, Hist1h1b, Hist1h2ae, Mki67
## Negative: Rps24, Malat1, Rps27, Rps29, Tpt1, Rplp1, Rps15a, Rpl12, Rpl23, Ccl5
## PC_ 2
## Positive: S100a6, S100a4, Lgals1, S100a10, Tmsb4x, Lgals3, Crip1, Gzmb, Gzma, Ccl5
## Negative: Top2a, Hist1h2ae, Hist1h3c, Hist1h2ab, Hist1h2ap, Hist1h4d, Nusap1, Hist2h2ac, Mki67, Hist1h1b
## PC_ 3
## Positive: Ccl5, Malat1, Klrk1, Ikzf2, Fcer1g, Klra7, Cenpf, Klre1, Ube2c, Nusap1
## Negative: Dapl1, Dut, Rplp1, Ptma, Rps8, Lgals3, 1500009L16Rik, Rps20, Rrm2, Hsp90ab1
## PC_ 4
## Positive: Dapl1, Ifi27l2a, Malat1, Ube2c, Cenpa, Cenpf, Ccr9, Fos, Igfbp4, Cd8b1
## Negative: Ccl5, Ctla2a, Ly6c2, Klre1, Hist1h2ae, Klra7, Rrm2, Dut, Hist1h1b, Hist1h2ap
## [1] "Contribution des gènes pour les PC"
## [1] "Heatmaps avec les 20 gènes contribuants le plus dans la PC"
Choose 11 CP for the continuation
## [1] "VV-B8R" "Ly49p-CD8ab" "VV-Ly49p-CD8aa" "Ly49p-CD8aa"
## [5] "VV-Ly49p-CD8ab" "Naive" "Ly49n"
## # A tibble: 14 × 7
## # Groups: cluster [7]
## p_val avg_log2FC pct.1 pct.2 p_val_adj cluster gene
## <dbl> <dbl> <dbl> <dbl> <dbl> <fct> <chr>
## 1 0 4.30 0.961 0.251 0 VV-B8R S100a4
## 2 0 4.13 0.743 0.217 0 VV-B8R Hist1h2ap
## 3 3.60e-217 1.03 0.934 0.633 5.53e-213 Ly49p-CD8ab Fos
## 4 4.13e-174 0.878 0.878 0.576 6.34e-170 Ly49p-CD8ab Dusp2
## 5 0 1.23 0.835 0.282 0 VV-Ly49p-CD8aa Ikzf2
## 6 5.22e-174 1.03 0.725 0.388 8.01e-170 VV-Ly49p-CD8aa Klra7
## 7 8.81e-229 1.21 0.854 0.327 1.35e-224 Ly49p-CD8aa Ikzf2
## 8 6.08e-175 1.20 0.948 0.65 9.32e-171 Ly49p-CD8aa Fos
## 9 1.28e-180 0.589 0.806 0.485 1.97e-176 VV-Ly49p-CD8ab Ms4a4c
## 10 2.06e-174 -1.06 0.249 0.551 3.16e-170 VV-Ly49p-CD8ab Itga4
## 11 8.51e-236 1.55 0.574 0.171 1.31e-231 Naive Dapl1
## 12 5.71e-242 1.02 0.904 0.65 8.75e-238 Naive Lef1
## 13 9.33e- 12 0.533 0.65 0.386 1.43e- 7 Ly49n Tnfaip3
## 14 3.44e- 10 -0.825 0.153 0.407 5.28e- 6 Ly49n Klre1
## Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck
##
## Number of nodes: 8310
## Number of edges: 266478
##
## Running Louvain algorithm...
## Maximum modularity in 10 random starts: 1.0000
## Number of communities: 1
## Elapsed time: 0 seconds
## Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck
##
## Number of nodes: 8310
## Number of edges: 266478
##
## Running Louvain algorithm...
## Maximum modularity in 10 random starts: 0.9500
## Number of communities: 5
## Elapsed time: 0 seconds
## Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck
##
## Number of nodes: 8310
## Number of edges: 266478
##
## Running Louvain algorithm...
## Maximum modularity in 10 random starts: 0.9231
## Number of communities: 7
## Elapsed time: 0 seconds
## Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck
##
## Number of nodes: 8310
## Number of edges: 266478
##
## Running Louvain algorithm...
## Maximum modularity in 10 random starts: 0.8995
## Number of communities: 9
## Elapsed time: 0 seconds
## Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck
##
## Number of nodes: 8310
## Number of edges: 266478
##
## Running Louvain algorithm...
## Maximum modularity in 10 random starts: 0.8820
## Number of communities: 9
## Elapsed time: 0 seconds
## Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck
##
## Number of nodes: 8310
## Number of edges: 266478
##
## Running Louvain algorithm...
## Maximum modularity in 10 random starts: 0.8672
## Number of communities: 11
## Elapsed time: 0 seconds
## Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck
##
## Number of nodes: 8310
## Number of edges: 266478
##
## Running Louvain algorithm...
## Maximum modularity in 10 random starts: 0.8538
## Number of communities: 12
## Elapsed time: 0 seconds
## Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck
##
## Number of nodes: 8310
## Number of edges: 266478
##
## Running Louvain algorithm...
## Maximum modularity in 10 random starts: 0.8421
## Number of communities: 13
## Elapsed time: 0 seconds
## Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck
##
## Number of nodes: 8310
## Number of edges: 266478
##
## Running Louvain algorithm...
## Maximum modularity in 10 random starts: 0.8305
## Number of communities: 13
## Elapsed time: 0 seconds
## Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck
##
## Number of nodes: 8310
## Number of edges: 266478
##
## Running Louvain algorithm...
## Maximum modularity in 10 random starts: 0.8193
## Number of communities: 14
## Elapsed time: 0 seconds
## Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck
##
## Number of nodes: 8310
## Number of edges: 266478
##
## Running Louvain algorithm...
## Maximum modularity in 10 random starts: 0.8095
## Number of communities: 14
## Elapsed time: 0 seconds
## Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck
##
## Number of nodes: 8310
## Number of edges: 266478
##
## Running Louvain algorithm...
## Maximum modularity in 10 random starts: 0.7998
## Number of communities: 15
## Elapsed time: 0 seconds
## Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck
##
## Number of nodes: 8310
## Number of edges: 266478
##
## Running Louvain algorithm...
## Maximum modularity in 10 random starts: 0.7912
## Number of communities: 16
## Elapsed time: 0 seconds
## Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck
##
## Number of nodes: 8310
## Number of edges: 266478
##
## Running Louvain algorithm...
## Maximum modularity in 10 random starts: 0.7840
## Number of communities: 18
## Elapsed time: 0 seconds
## Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck
##
## Number of nodes: 8310
## Number of edges: 266478
##
## Running Louvain algorithm...
## Maximum modularity in 10 random starts: 0.7787
## Number of communities: 18
## Elapsed time: 0 seconds
## Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck
##
## Number of nodes: 8310
## Number of edges: 266478
##
## Running Louvain algorithm...
## Maximum modularity in 10 random starts: 0.7715
## Number of communities: 20
## Elapsed time: 0 seconds
## Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck
##
## Number of nodes: 8310
## Number of edges: 266478
##
## Running Louvain algorithm...
## Maximum modularity in 10 random starts: 0.8672
## Number of communities: 11
## Elapsed time: 0 seconds
## [1] "0" "1" "2" "3" "4" "5" "6" "7" "8" "9" "10"
## # A tibble: 21 × 7
## # Groups: cluster [11]
## p_val avg_log2FC pct.1 pct.2 p_val_adj cluster gene
## <dbl> <dbl> <dbl> <dbl> <dbl> <fct> <chr>
## 1 0 1.42 0.966 0.601 0 0 Fos
## 2 0 1.22 0.949 0.624 0 0 Fosb
## 3 4.57e-180 1.04 0.734 0.388 7.01e-176 1 Klra7
## 4 7.20e-140 0.907 0.628 0.312 1.10e-135 1 Klrk1
## 5 1.90e- 98 -1.14 0.219 0.502 2.92e- 94 2 Itga4
## 6 3.96e-278 1.66 0.595 0.165 6.08e-274 3 Dapl1
## 7 1.43e-249 1.03 0.903 0.649 2.19e-245 3 Lef1
## 8 6.99e-104 0.816 0.56 0.258 1.07e- 99 4 Gzmm
## 9 8.63e- 81 0.527 0.848 0.547 1.32e- 76 4 Ms4a4c
## 10 1.32e-218 2.95 0.906 0.297 2.02e-214 5 S100a4
## # … with 11 more rows